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Faster an simpler LargestChainDescriptor.
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@johnmay
johnmay committed Feb 11, 2016
1 parent 7bcbe4f commit 6daeadd
Showing 1 changed file with 34 additions and 113 deletions.
147 changes: 34 additions & 113 deletions .../src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java
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Expand Up @@ -18,25 +18,21 @@
*/
package org.openscience.cdk.qsar.descriptors.molecular;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.aromaticity.Aromaticity;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.exception.NoSuchAtomException;
import org.openscience.cdk.graph.SpanningTree;
import org.openscience.cdk.graph.AllPairsShortestPaths;
import org.openscience.cdk.graph.Cycles;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.qsar.AbstractMolecularDescriptor;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.qsar.result.IntegerResult;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

import java.util.ArrayList;
import java.util.List;
import java.util.HashSet;
import java.util.Set;

/**
* Class that returns the number of atoms in the largest chain.
Expand Down Expand Up @@ -168,76 +164,32 @@ private DescriptorValue getDummyDescriptorValue(Exception e) {
*/
@Override
public DescriptorValue calculate(IAtomContainer atomContainer) {
IAtomContainer container;
try {
container = (IAtomContainer) atomContainer.clone();
} catch (CloneNotSupportedException e) {
return getDummyDescriptorValue(e);
}

//logger.debug("LargestChainDescriptor");
boolean[] originalFlag4 = new boolean[container.getAtomCount()];
for (int i = 0; i < originalFlag4.length; i++) {
originalFlag4[i] = container.getAtom(i).getFlag(CDKConstants.VISITED);
}
if (checkRingSystem) {
IRingSet rs;
try {
rs = new SpanningTree(container).getBasicRings();
} catch (NoSuchAtomException e) {
return getDummyDescriptorValue(e);
}
for (int i = 0; i < container.getAtomCount(); i++) {
if (rs.contains(container.getAtom(i))) {
container.getAtom(i).setFlag(CDKConstants.ISINRING, true);
}
}
}
if (checkRingSystem)
Cycles.markRingAtomsAndBonds(atomContainer);

if (checkAromaticity) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(container);
Aromaticity.cdkLegacy().apply(container);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
// make a subset molecule only including acyclic non-hydrogen atoms
final Set<IAtom> included = new HashSet<>();
for (IAtom atom : atomContainer.atoms()) {
if (!atom.isInRing() && atom.getAtomicNumber() != 1)
included.add(atom);
}
IAtomContainer subset = subsetMol(atomContainer, included);

// get rid of hydrogens in our local copy
container = AtomContainerManipulator.removeHydrogens(container);
AllPairsShortestPaths apsp = new AllPairsShortestPaths(subset);

int largestChainAtomsCount = 0;
//IAtom[] atoms = container.getAtoms();
ArrayList<IAtom> startSphere;
ArrayList<IAtom> path;

//logger.debug("Set all atoms to Visited False");
for (int i = 0; i < container.getAtomCount(); i++) {
for (IAtom a : container.atoms()) a.setFlag(CDKConstants.VISITED, false);

IAtom atomi = container.getAtom(i);
// chain sp3
//logger.debug("atom:"+i+" maxBondOrder:"+container.getMaximumBondOrder(atoms[i])+" Aromatic:"+atoms[i].getFlag(CDKConstants.ISAROMATIC)+" Ring:"+atoms[i].getFlag(CDKConstants.ISINRING)+" FormalCharge:"+atoms[i].getFormalCharge()+" Charge:"+atoms[i].getCharge()+" Flag:"+atoms[i].getFlag(CDKConstants.VISITED));
if ((!atomi.getFlag(CDKConstants.ISAROMATIC) && !atomi.getFlag(CDKConstants.ISINRING))
& !atomi.getFlag(CDKConstants.VISITED)) {
//logger.debug("...... -> containercepted");
startSphere = new ArrayList<IAtom>();
path = new ArrayList<IAtom>();
startSphere.add(atomi);
try {
breadthFirstSearch(container, startSphere, path);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
if (path.size() > largestChainAtomsCount) {
largestChainAtomsCount = path.size();
}
int max = 0;
int numAtoms = subset.getAtomCount();
for (int i = 0; i < numAtoms; i++) {
for (int j = i+1; j < numAtoms; j++) {
int len = apsp.from(i).pathTo(j).length;
if (len > max)
max = len;
}

}

return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(
largestChainAtomsCount), getDescriptorNames());
max), getDescriptorNames());
}

/**
Expand All @@ -256,50 +208,6 @@ public IDescriptorResult getDescriptorResultType() {
return new IntegerResult(1);
}

/**
* Performs a breadthFirstSearch in an AtomContainer starting with a
* particular sphere, which usually consists of one start atom, and searches
* for a pi system.
*
* @param container The AtomContainer to
* be searched
* @param sphere A sphere of atoms to
* start the search with
* @param path A ArrayList which stores the atoms belonging to the pi system
* @throws org.openscience.cdk.exception.CDKException
* Description of the
* Exception
*/
private void breadthFirstSearch(IAtomContainer container, List<IAtom> sphere, List<IAtom> path) throws CDKException {
IAtom atom;
IAtom nextAtom;
List<IAtom> newSphere = new ArrayList<IAtom>();
//logger.debug("Start of breadthFirstSearch");
for (int i = 0; i < sphere.size(); i++) {
atom = sphere.get(i);
//logger.debug("BreadthFirstSearch around atom " + (atomNr + 1));
List<IBond> bonds = container.getConnectedBondsList(atom);
for (IBond bond : bonds) {
nextAtom = bond.getConnectedAtom(atom);
if ((!nextAtom.getFlag(CDKConstants.ISAROMATIC) && !nextAtom.getFlag(CDKConstants.ISINRING))
& !nextAtom.getFlag(CDKConstants.VISITED)) {
//logger.debug("BDS> AtomNr:"+container.getAtomNumber(nextAtom)+" maxBondOrder:"+container.getMaximumBondOrder(nextAtom)+" Aromatic:"+nextAtom.getFlag(CDKConstants.ISAROMATIC)+" FormalCharge:"+nextAtom.getFormalCharge()+" Charge:"+nextAtom.getCharge()+" Flag:"+nextAtom.getFlag(CDKConstants.VISITED));
path.add(nextAtom);
//logger.debug("BreadthFirstSearch is meeting new atom " + (nextAtomNr + 1));
nextAtom.setFlag(CDKConstants.VISITED, true);
if (container.getConnectedBondsCount(nextAtom) > 1) {
newSphere.add(nextAtom);
}
} else {
nextAtom.setFlag(CDKConstants.VISITED, true);
}
}
}
if (newSphere.size() > 0) {
breadthFirstSearch(container, newSphere, path);
}
}

/**
* Gets the parameterNames attribute of the LargestPiSystemDescriptor object.
*
Expand All @@ -323,4 +231,17 @@ public String[] getParameterNames() {
public Object getParameterType(String name) {
return true;
}

private static IAtomContainer subsetMol(IAtomContainer mol, Set<IAtom> include) {
IAtomContainer cpy = mol.getBuilder().newInstance(IAtomContainer.class, mol.getAtomCount(), mol.getBondCount(), 0, 0);
for (IAtom atom : mol.atoms()) {
if (include.contains(atom))
cpy.addAtom(atom);
}
for (IBond bond : mol.bonds()) {
if (include.contains(bond.getAtom(0)) && include.contains(bond.getAtom(1)))
cpy.addBond(bond);
}
return cpy;
}
}

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